genes.with.TSS.covered: genes.with.TSS.covered
In favorov/differential.coverage: Differential Coverage package

Description Usage Arguments Details Value Author(s) See Also

Generates list of genes that start inside a given set of intervals

genes.with.TSS.covered(
  noodles,
  flanks = 0,
  genes = NA,
  genome.id = "gencode19"
)

`noodles`	the `GRanges` list of intervals to look TSS in
`flanks`	lenght to inflate the noddles by before the search; if >0, the seqlengths information is to be set in `noodles`
`genes`	it is GRandes oject with the annotation genes. The gene_name matadata field is almost required, it passes the gene name to form output. The default is NA that means that the function will call `get.Known.Gene.List`
`genome.id`	is genome.annotation.id to call `get.Known.Gene.List`

After the noodles (the set of intervals to search TSS in) are inflated by flanks, we look for all the TSS that start inside the (inflated) intervals. Genes are provided by parameter or they are returned by get.Known.Gene.List for genome_id. If the noodles has p.value and/or fdr metadata, we ascribe the data of the interval to the retrieved gene. If there a gene refers to a set of noodles, it has min ascribed. The ishyper data is also transferred to gene, if it is not contradictory.

GRanges object that is the list of the genes we look for - the object is not co-indexed with noodles parameter

Alexander Favorov, favorov@sensi.org

differential.coverage

favorov/differential.coverage documentation built on Feb. 18, 2022, 5:50 p.m.